Bug fixes #102
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| name: AmpSeeker-fastqauto | |
| on: pull_request | |
| jobs: | |
| run-workflow: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.9'] | |
| steps: | |
| - name: Set up python3 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Test workflow | |
| uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c | |
| with: | |
| directory: '.test' | |
| snakefile: 'workflow/Snakefile' | |
| args: '--cores 4 --use-conda --conda-cleanup-pkgs cache --configfile .test/config/config_fastqauto.yaml' | |
| stagein: | |
| " | |
| wget https://vectorbase.org/common/downloads/release-66/AgambiaePEST/fasta/data/VectorBase-66_AgambiaePEST_Genome.fasta -q -O - | sed 's/AgamP4_//g' > .test/resources/reference/AgamP4.fa && | |
| cp config/ag-vampir.bed .test/config/ag-vampir.bed && | |
| cp -r docs/ .test/docs/ && | |
| conda config --set channel_priority flexible | |
| " |